2A66

Human Liver Receptor Homologue DNA-Binding Domain (hLRH-1 DBD) in Complex with dsDNA from the hCYP7A1 Promoter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of the Human LRH-1 DBD-DNA Complex Reveals Ftz-F1 Domain Positioning is Required for Receptor Activity.

Solomon, I.H.Hager, J.M.Safi, R.McDonnell, D.P.Redinbo, M.R.Ortlund, E.A.

(2005) J Mol Biol 354: 1091-1102

  • DOI: 10.1016/j.jmb.2005.10.009
  • Primary Citation of Related Structures:  
    2A66

  • PubMed Abstract: 
  • The DNA-binding and ligand-binding functions of nuclear receptors are localized to independent domains separated by a flexible hinge. The DNA-binding domain (DBD) of the human liver receptor homologue-1 (hLRH-1), which controls genes central to devel ...

    The DNA-binding and ligand-binding functions of nuclear receptors are localized to independent domains separated by a flexible hinge. The DNA-binding domain (DBD) of the human liver receptor homologue-1 (hLRH-1), which controls genes central to development and metabolic homeostasis, interacts with monomeric DNA response elements and contains an Ftz-F1 motif that is unique to the NR5A nuclear receptor subfamily. Here, we present the 2.2A resolution crystal structure of the hLRH-1 DBD in complex with duplex DNA, and elucidate the sequence-specific DNA contacts essential for the ability of LRH-1 to bind to DNA as a monomer. We show that the unique Ftz-F1 domain folds into a novel helix that packs against the DBD but does not contact DNA. Mutations expected to disrupt the positioning of the Ftz-F1 helix do not eliminate DNA binding but reduce the transcriptional activity of full-length LRH-1 significantly. Moreover, we find that altering the Ftz-F1 helix positioning eliminates the enhancement of LRH-1-mediated transcription by the coactivator GRIP1, an action that is associated primarily with the distantly located ligand-binding domain (LBD). Taken together, these results indicate that subtle structural changes in a nuclear receptor DBD can exert long-range functional effects on the LBD of a receptor, and significantly impact transcriptional regulation.


    Organizational Affiliation

    Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Orphan nuclear receptor NR5A2A113Homo sapiensMutation(s): 0 
Gene Names: NR5A2B1FCPFFTF
Find proteins for O00482 (Homo sapiens)
Explore O00482 
Go to UniProtKB:  O00482
NIH Common Fund Data Resources
PHAROS  O00482
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3'B12Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3'C12Homo sapiens
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download CCD File 
      A
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      ACT
      Query on ACT

      Download CCD File 
      A
      ACETATE ION
      C2 H3 O2
      QTBSBXVTEAMEQO-UHFFFAOYSA-M
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.20 Å
      • R-Value Free: 0.226 
      • R-Value Work: 0.196 
      • R-Value Observed: 0.196 
      • Space Group: P 43
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 40.77α = 90
      b = 40.77β = 90
      c = 104.85γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      MOLREPphasing
      CNSrefinement
      PDB_EXTRACTdata extraction
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2005-12-06
        Type: Initial release
      • Version 1.1: 2008-04-30
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2017-10-11
        Changes: Refinement description